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An integrated Riverine Environmental Flow Decision Support System (REFDSS) to evaluate the ecological effects of alternative flow scenarios on river ecosystems
In regulated rivers, managers must evaluate competing flow release scenarios that attempt to balance both human and natural needs. Meeting these natural flow needs is complex due to the myriad of interacting physical and hydrological factors that affect ecosystems. Tools that synthesize the voluminous scientific data and models on these factors will facilitate management of these systems. Here, we present the Riverine Environmental Flow Decision Support System (REFDSS), a tool that enables evaluation of competing flow scenarios and other variables on instream habitat. We developed a REFDSS for the Upper Delaware River, USA, a system that is regulated by three headwater reservoirs. This version of the REFDSS has the ability to integrate any set of spatially explicit data and synthesizes modeled discharge for three competing management scenarios, flow-specific 2-D hydrodynamic modeled estimates of local hydrologic conditions (e.g., depth, velocity, shear stress, etc.) at a fine pixel-scale (1 m 2 ), and habitat suitability criteria (HSC) for a variety of taxa. It contains all individual model outputs, computationally integrates these data, and outputs the amount of potentially available habitat for a suite of species of interest under each flow release scenario. Users have the flexibility to change the time period of interest and vary the HSC. The REFDSS was developed to enable side-by-side evaluation of different flow management scenarios and their effects on potential habitat availability, allowing managers to make informed decisions on the best flow scenarios. An exercise comparing two alternative flow scenarios to a baseline scenario for several key species is presented. The Upper Delaware REFDSS was robust to minor changes in HSC (± 10 %). The general REFDSS platform was developed as a user-friendly Windows desktop application that was designed to include other potential parameters of interest (e.g., temperature) and for transferability to other riverine systems.
Cross-kingdom amplification using Bacteria-specific primers: Complications for studies of coral microbial ecology
PCR amplification of pure bacterial DNA is vital to the study of bacterial interactions with corals. Commonly used Bacteria -specific primers 8F and 27F paired with the universal primer 1492R amplify both eukaryotic and prokaryotic rRNA genes. An alternative primer set, 63F/1542R, is suggested to resolve this problem.
Some ecological relations of Pseudomonas aeruginosa to Clostridium botulinum type C
No abstract available.
Drainage-basis-scale geomorphic analysis to determine refernce conditions for ecologic restoration-Kissimmee River, Florida
Major controls on the retention, distribution, and discharge of surface water in the historic (precanal) Kissimmee drainage basin and river were investigated to determine reference conditions for ecosystem restoration. Precanal Kissimmee drainage-basin hydrology was largely controlled by landforms derived from relict, coastal ridge, lagoon, and shallow-shelf features; widespread carbonate solution depressions; and a poorly developed fluvial drainage network. Prior to channelization for flood control, the Kissimmee River was a very low gradient, moderately meandering river that flowed from Lake Kissimmee to Lake Okeechobee through the lower drainage basin. We infer that during normal wet seasons, river discharge rapidly exceeded Lake Okeechobee outflow capacity, and excess surface water backed up into the low-gradient Kissimmee River. This backwater effect induced bankfull and peak discharge early in the flood cycle and transformed the flood plain into a shallow aquatic system with both lacustrine and riverine characteristics. The large volumes of surface water retained in the lakes and wetlands of the upper basin maintained overbank flow conditions for several months after peak discharge. Analysis indicates that most of the geomorphic work on the channel and flood plain occurred during the frequently recurring extended periods of overbank discharge and that discharge volume may have been significant in determining channel dimensions. Comparison of hydrogeomorphic relationships with other river systems identified links between geomorphology and hydrology of the precanal Kissimmee River. However, drainage-basin and hydraulic geometry models derived solely from general populations of river systems may produce spurious reference conditions for restoration design criteria.
Physical and ecologic features of the Sagadahoc Bay Tidal Flat, Georgetown, Maine
Sagadahoc Bay is open to the ocean at the south and has no significant fresh-water stream entering it. The intertidal zone is roughly a mile long by half a mile wide; most of it is made up of medium to fine sand, but organic-rich mud characterizes the head of the flat and the protected coves. Refraction-seismograph surveys showed that the bedrock surface lies 30 to 200 feet below the surface of the tidal flat and that it is irregular and fluted longitudinally. Repeated surveys indicate that the intertidal flat builds up and cuts down but is apparently in equilibrium with the present sea level. The sediment that fills the bay came from the sea. Waves and tidal currents tend to move it landward; storms accelerate this, or reverse the direction of movement, depending on the characteristics of the storm. Tidal- and wave-generated currents 0.1 foot above the bottom range in velocity from 0.35 to 0.82 foot per second on incoming tides and from 0.20 to 0.58 foot per second on ebbing tides. Incoming tides float large quantities of sand landward; ebbing tides never carry floating sand. Two distinctive and extensive Mya shell-pavement layers were found at depths of roughly 2 and 3 feet below the present surface of the tidal flat. The lower layer is approximately 1,000 years old according to a radiocarbon age determination of its Mya shells. It is suggested that these shell layers formed by sluicing away of a layer of sand about 2 feet thick, which had been thrown into loose packing by an earthquake at high tide. The earth shock induced a submarine slide of the sand in the outer part of the bay, which oversteepened the profile of the sand headward nearly to the head of the bay. Mya and other shells settled through the layer of quicksand while the sand was running out seaward. Living in the intertidal zone is the usual assemblage of clams, gastropods, crustaceans, worms, and seaweeds found on most northern New England tidal flats. The Mya arenaria population is decreasing, but in general myas are more numerous in the muddy areas than in the sandy areas. They grow more rapidly in the sand, though in the past decade there has been no significant renewal of the Mya population in the sandy part of the flat. Macoma balthica inhabits the muddy areas, whereas Ensis, Spisula, and Arctica are restricted to the low-tide zone and the shallow water below. Gemma gemma grows in great abundance in the sandy part of the flat but is rare in the muddy parts. Small shrimp and green crabs are common. The calcareous shells of these animals are all potential fossils, but the shrimp and crab exoskeletons are not, for their tests are rapidly decomposed in this environment. Other potential fossils are wood and bark, acorn caps, conifer cones, leaves of deciduous trees, seeds, and occasionally even grass stems and pieces of eel grass. All these are reasonably well preserved in the constant reducing environment that prevails an inch or two below the surface. An inverse relationship exists between the abundances of Mya arenaria and Gemma gemma. Cores and test pits show that gemmas are more numerous on the Sagadahoc flat now than they have been in the recent past (estimated 10–100 years). Gemmas are the dominant mollusk in the sandy part of the flat now that the myas are so extremely rare. The speculation is that gemmas became dominant largely because the Mya population was greatly reduced by intensive digging during and just after the last war and through depredations by green crabs. Possibly the warming climate has favored the gemmas selectively. The writer infers that the gemmas are a serious competitor of the myas and that the gemmas now starve out Mya spat, which is known to be carried into the bay each spring and fall. Two recommendations are made: (1) determining under controlled laboratory conditions the food requirements of Gemma and the density of Gemma population that will permit survival of Mya larvae from set through a stage that will assure maturation; and (2) killing off a large percentage of the Gemma population and observing whether or not a natural set of Mya occurs. Gemmas can be killed quickly under a flame shield such as is used to soften asphalt-sand mixtures in street paving. Inasmuch as gemmas are ovoviviparous they should not repopulate the flat rapidly.
Trophic ecology of juvenile lean and siscowet lake charr (Salvelinus namaycush) in Lake Superior: Assessing for potential competition
We investigated the spatial overlap, diet, isotopic niche, and growth of juvenile lean and siscowet lake charr ( Salvelinus namaycush ) in Lake Superior to address concerns of potential competition with implications to the study of resource polymorphism. Catch data revealed the greatest levels of sympatry in waters from 40 to 60 m. Juvenile lean and siscowet diet changed ontogenetically with Mysis being the dominant prey item for the smallest lake charr but differentiating with onset of piscivory. As ecotypes increased in size, lean diets became dominated by pelagic prey, whereas siscowets had equal proportions of benthic and pelagic prey. Isotopic niche overlap declined between ecotypes coincident with siscowet lake charr shifting to deeper habitats around 400 mm. Lean and siscowet exhibited different growth trajectories. However, length at age-4 declined in parallel for both ecotypes with no trend in condition suggesting that lake charr growth is sensitive to prey biomass and unlikely related to competition. Our findings indicate minimal evidence of competition and support the concept that multiple sympatric ecotypes of lake charr in Lake Superior are maintained by resource polymorphism.
Energy sources and ecological role of crayfishes in an Ozark stream: Insights from stable isotopes and gut analysis
Energy sources for the crayfishes Orconectes luteus and O. punctimanus in the Jacks Fork River, Missouri, were quantified using stable isotopes (??13C and ??15N) and gut-content analysis. A dual-isotope mixing model indicated that about two thirds of crayfish production originated from allochthonous carbon sources, and 30-50% of crayfish production was derived from direct consumption of animal matter. Young-of-the-year crayfishes and adult O. luteus were more carnivorous than the larger adult O. punctimanus. Contributions of energy sources determined using the stable isotope mixing model were similar to results of gut-content analysis corrected for differential assimilation of dietary components. Proportions of crayfish production attributed to animal matter by these two methods were four to five times greater than estimates derived from uncorrected gut-content analysis. Unadjusted gut-content analysis overestimated the percentage of crayfish production from feeding directly on detritus. Production-based calculations of crayfish food consumption rates indicated that crayfishes were the dominant consumers of benthic invertebrates, detritus, and algae and may strongly influence lower trophic levels, organic matter processing, and energy flow in this system.
Ecological correlates of variable organ sizes and fat loads in the most northerly-wintering shorebirds
Shorebirds at northern latitudes during the nonbreeding season typically carry relatively large lipid stores and exhibit an up-regulation of lean tissues associated with digestion and thermogenesis. Intraspecific variation in these tissues across sites primarily reflects differences in environmental conditions. Rock (Calidris ptilocnemis (Coues, 1873)) and Purple (Calidris maritima (Brünnich, 1764)) sandpipers are closely related species having the most northerly nonbreeding distributions among shorebirds, living at latitudes up to 61°N in Cook Inlet, Alaska, and up to 71°N in northern Norway, respectively. Cook Inlet is the coldest known site used by nonbreeding shorebirds, and the region’s mudflats annually experience extensive coverage of foraging sites by sea and shore-fast ice. Accordingly, Rock Sandpipers increase their fat stores to nearly 20% of body mass during winter. In contrast, Purple Sandpipers exploit predictably ice-free rocky intertidal foraging sites and maintain low (<6.5%) fat stores. Rock Sandpipers increase the mass of lean tissues from fall to winter, including contour feathers, stomach, and liver components. They also have greater lean pectoralis and supracoracoideus muscle and liver and kidney tissues compared with Purple Sandpipers in winter. This demonstrates a combined emphasis on digestive processes and thermogenesis, whereas Purple Sandpipers primarily augment organs associated with digestive processes. The high winter fat loads and increased lean tissues of Rock Sandpipers in Cook Inlet reflect the region’s persistent cold and abundant but sporadically unavailable food resources.
Ecology of the Lake Huron fish community, 1970-1999
We review the status of the Lake Huron fish community between 1970 and 1999 and explore the effects of key stressors. Offshore waters changed little in terms of nutrient enrichment, while phosphorus levels declined in inner Saginaw Bay. Introduced mussels ( Dreissena spp.) proliferated and may have caused a decline in Diporeia spp. This introduction could have caused a decline in lake whitefish ( Coregonus clupeaformis ) growth and condition, with serious repercussions for commercial fisheries. Bythotrephes , an exotic predatory cladoceran, and other new exotics may be influencing the fish community. Sea lampreys ( Petromyzon marinus ) remained prevalent, but intensive control efforts on the St. Mary's River may reduce their predation on salmonines. Overfishing was less of a problem than in the past, although fishing continued to reduce the amount of lake trout ( Salvelinus namaycush ) spawning biomass resulting from hatchery-reared fish planted to rehabilitate this species. Massive stocking programs have increased the abundance of top predators, but lake trout were rehabilitated in only one area. Successful lake trout rehabilitation may require lower densities of introduced pelagic prey fish than were seen in the 1990s, along with continued stocking of hatchery-reared lake trout and control of sea lamprey. Such reductions in prey fish could limit Pacific salmon ( Oncorhynchus spp.) fisheries.
Factors of ecologic succession in oligotrophic fish communities of the Laurentian Great Lakes
Oligotrophic fish communities of the Great Lakes have undergone successive disruptions since the mid-1800s. Major contributing factors have been intensive selective fisheries, extreme modification of the drainage, invasion of marine species, and progressive physical–chemical changes of the lake environments. Lake Ontario was the first to be affected as its basin was settled and industrialized earliest, and it was the first to be connected by canals to the mid-Atlantic where the alewife ( Alosa pseudoharengus ) and sea lamprey ( Petromyzon marinus ) which ultimately became established in the Great Lakes were abundant. Oligotrophic fish communities were successively disrupted in Lakes Erie, Huron, Michigan, and Superior as the affects of population growth, industrialization, and marine invaders spread upward in the Laurentian drainage.The degree and sequence of response of families offish and species within families differed for each factor, but the sequence of change among families and species has been the same in response to each factor as it affected various lakes at different times. The ultimate result of the disruption of fish communities has been a reduction of productivity of oligotrophic species that ranges from extreme in Lake Ontario to moderate in Lake Superior, and which has reached a state of instability and rapid change in the upper three Great Lakes by the rnid-1900s similar to the situation in Lake Ontario in the mid-1800s. Since oligotrophic species (primarily salmonines, coregonines, and deepwater cottids) are the only kinds of fish that fully occupied the entire volume of the deepwater Great Lakes (Ontario, Huron, Michigan, and Superior), the fish biomass of these lakes has been reduced as various species declined or disappeared. In Lake Erie, which is shallow, and in the shallow bays of the deep lakes, oligotrophic species were replaced by mesotrophic species, primarily percids, which have successively increased and declined. All oligotrophic species are greatly reduced or extinct in lakes Ontario and Erie, and are in various stages of decline in lakes Huron, Michigan, and Superior, from greatest to least, respectively. The percids appear to be near the end of their sequence of succession in lakes Erie, Ontario, and Huron (primarily Saginaw Bay) where only the yellow perch ( Perca flavescens ) remains abundant. The yellow perch appears to be on the brink of decline in Lake Erie, which has been more severely influenced by water quality change than the other lakes.
Trophic ecology of largemouth bass and northern pike in allopatric and sympatric assemblages in northern boreal lakes
Largemouth bass ( Micropterus salmoides ) and northern pike ( Esox lucius ) are top predators in the food chain in most aquatic environments that they occupy; however, limited information exists on species interactions in the northern reaches of largemouth bass distribution. We investigated the seasonal food habits of allopatric and sympatric assemblages of largemouth bass and northern pike in six interior lakes within Voyageurs National Park, Minnesota. Percentages of empty stomachs were variable for largemouth bass (38-54%) and northern pike (34.7-66.7%). Fishes (mainly yellow perch, Perca flavescens ) comprised greater than 60% (mean percent mass, MPM) of the northern pike diet during all seasons in both allopatric and sympatric assemblages. Aquatic insects (primarily Odonata and Hemiptera) were important in the diets of largemouth bass in all communities (0.0-79.7 MPM). Although largemouth bass were observed in the diet of northern pike, largemouth bass apparently did not prey on northern pike. Seasonal differences were observed in the proportion of aquatic insects ( P = 0.010) and fishes ( P = 0.023) in the diets of northern pike and largemouth bass. Based on three food categories, jackknifed classifications correctly classified 77 and 92% of northern pike and largemouth bass values, respectively. Percent resource overlap values were biologically significant (greater than 60%) during at least one season in each sympatric assemblage, suggesting some diet overlap.
Ecological correlates of mate fidelity in two Arctic-breeding sandpipers
Monogamous birds exhibit considerable interspecific variation in rates of mate fidelity between years, but the reasons for this variation are still poorly understood. In a 4-year study carried out in western Alaska, mate-fidelity rates in Semipalmated Sandpipers ( Calidris pusilla ; mate fidelity was 47% among pairs where at least one mate returned and 94% among pairs where both mates returned) were substantially higher than in Western Sandpipers ( Calidris mauri ; 25 and 67%, respectively), despite the similar breeding biology of these sibling species. Divorce was not a response to nesting failure in Western Sandpipers, and mate change had no effect on the reproductive performance of either species. Nor were mate-fidelity rates related to differential rates of breeding dispersal, because the species did not differ in site fidelity. Reunited pairs and males that changed mates showed strong site tenacity, while females that changed mates moved farther. Differences in local survival rates or habitat are also unlikely to explain mate fidelity, since the two species did not differ in local survival rates, ϕ (Western Sandpipers: ϕ hat = 0.57 ± 0.05 (mean ± SE), Semipalmated Sandpipers: ϕ hat = 0.66 ± 0.06), and they bred in the same area, sometimes using the same nest cups. Although we were able to reject the above explanations, it was not possible to determine whether mate retention was lower in Western Sandpipers than in Semipalmated Sandpipers because of interspecific differences in mating tactics, time constraints imposed by migration distance, or a combination of these factors. Western Sandpipers exhibited greater sexual size dimorphism, but also migrated for shorter distances and tended to nest earlier and more asynchronously than Semipalmated Sandpipers. Finally, we show that conventional methods underestimate divorce rates, and interspecific comparisons may be biased if breeding-dispersal and recapture rates are not considered.
Nutritional ecology of a fossorial herbivore: protein N and energy value of winter caches made by the northern pocket gopher, Thomomys talpoides
Northern pocket gophers ( Thomomys talpoides ) are fossorial herbivores that excavate belowground plant parts for food. In subalpine areas during autumn and winter, pocket gophers hoard plant parts in caches placed in or under snow. We examined the size and composition of 17 nival caches and tested the hypotheses that (i) cached food can provide complete energy and protein N sustenance during typical periods when burrowing is precluded by soil conditions, and (ii) cached food is a random sample of items encountered by burrowing gophers during tunnel excavation. Our data indicate that caches provide substantially more energy than protein in terms of a pocket gopher's daily maintenance requirements. Nevertheless, quantities stored are sufficient to allow individuals to endure commonly encountered adverse environmental conditions without entering negative energy or protein balance. Analysis of stomach contents and a comparison of cache composition to availability of plant species suggests that gophers consume high-protein items as they are encountered, and store low-protein items in caches.
Efficient 3D movement-based kernel density estimator and application to wildlife ecology
We describe an efficient implementation of a 3D movement-based kernel density estimator for determining animal space use from discrete GPS measurements. This new method provides more accurate results, particularly for species that make large excursions in the vertical dimension. The downside of this approach is that it is much more computationally expensive than simpler, lower-dimensional models. Through a combination of code restructuring, parallelization and performance optimization, we were able to reduce the time to solution by up to a factor of 1000x, thereby greatly improving the applicability of the method.
Defining ecological drought for the 21st century
No abstract available.
Building a multi-scaled geospatial temporal ecology database from disparate data sources: Fostering open science through data reuse
Although there are considerable site-based data for individual or groups of ecosystems, these datasets are widely scattered, have different data formats and conventions, and often have limited accessibility. At the broader scale, national datasets exist for a large number of geospatial features of land, water, and air that are needed to fully understand variation among these ecosystems. However, such datasets originate from different sources and have different spatial and temporal resolutions. By taking an open-science perspective and by combining site-based ecosystem datasets and national geospatial datasets, science gains the ability to ask important research questions related to grand environmental challenges that operate at broad scales. Documentation of such complicated database integration efforts, through peer-reviewed papers, is recommended to foster reproducibility and future use of the integrated database. Here, we describe the major steps, challenges, and considerations in building an integrated database of lake ecosystems, called LAGOS (LAke multi-scaled GeOSpatial and temporal database), that was developed at the sub-continental study extent of 17 US states (1,800,000 km 2 ). LAGOS includes two modules: LAGOS GEO , with geospatial data on every lake with surface area larger than 4 ha in the study extent (~50,000 lakes), including climate, atmospheric deposition, land use/cover, hydrology, geology, and topography measured across a range of spatial and temporal extents; and LAGOS LIMNO , with lake water quality data compiled from ~100 individual datasets for a subset of lakes in the study extent (~10,000 lakes). Procedures for the integration of datasets included: creating a flexible database design; authoring and integrating metadata; documenting data provenance; quantifying spatial measures of geographic data; quality-controlling integrated and derived data; and extensively documenting the database. Our procedures make a large, complex, and integrated database reproducible and extensible, allowing users to ask new research questions with the existing database or through the addition of new data. The largest challenge of this task was the heterogeneity of the data, formats, and metadata. Many steps of data integration need manual input from experts in diverse fields, requiring close collaboration.